@Article{McMurdie2013,
    author = {Paul J. McMurdie and Susan Holmes},
    journal = {PLoS ONE},
    pages = {e61217},
    title = {phyloseq: An R package for reproducible interactive analysis and graphics of microbiome census data},
    volume = {8},
    number = {4},
    year = {2013},
    url = {http://dx.plos.org/10.1371/journal.pone.0061217},
  }

@Manual{Caballero_2013,
  title =	 {df2json: Convert a dataframe to JSON},
  author =	 {Nacho Caballero},
  year =	 2013,
  note =	 {R package version 0.0.2},
  url =		 {http://CRAN.R-project.org/package=df2json},
}

@Article{Chessel_2004,
  title =	 {The ade4 package-{I}- {O}ne-table methods},
  author =	 {D. Chessel and A.B. Dufour and J. Thioulouse},
  journal =	 {R News},
  year =	 2004,
  volume =	 4,
  pages =	 {5-10},
}

@Manual{Couture-Beil_2014,
  title =	 {rjson: JSON for R},
  author =	 {Alex Couture-Beil},
  year =	 2014,
  note =	 {R package version 0.2.15},
  url =		 {http://CRAN.R-project.org/package=rjson},
}

@Manual{Dejean_2014,
  title =	 {mixOmics: Omics Data Integration Project},
  author =	 {Sebastien Dejean and Ignacio Gonzalez and Kim-Anh Le
                  Cao with contributions from Pierre Monget and Jeff
                  Coquery and FangZou Yao and Benoit Liquet and
                  Florian Rohart},
  year =	 2014,
  note =	 {R package version 5.0-3},
  url =		 {http://CRAN.R-project.org/package=mixOmics},
}

@Article{Dray_2007,
  title =	 {The ade4 package: implementing the duality diagram
                  for ecologists},
  author =	 {S. Dray and A.B. Dufour},
  journal =	 {Journal of Statistical Software},
  year =	 2007,
  volume =	 22,
  pages =	 {1-20},
  number =	 4,
}

@Article{Dray_2007a,
  title =	 {The ade4 package-{II}: {T}wo-table and {K}-table
                  methods.},
  author =	 {S. Dray and A.B. Dufour and D. Chessel},
  journal =	 {R News},
  year =	 2007,
  volume =	 7,
  number =	 2,
  pages =	 {47-52},
}

@Article{Faust15,
  author =	 {Karoline Faust and Leo Lahti and Didier Gonze and
                  Willem M de Vos and Jeroen Raes},
  title =	 {Metagenomics meets time series analysis: unraveling
                  microbial community dynamics},
  journal =	 {Current Opinion in Microbiology},
  year =	 2015,
  volume =	 25,
  pages =	 {56--66},
  month =	 6,
  url =
                  {http://www.sciencedirect.com/science/article/pii/S1369527415000478},
  doi =		 {10.1016/j.mib.2015.04.004},
  annote =	 {Shared first author.}
}

@article{HalfvarsonNatMicro,
  author =	 {Jonas Halfvarson and Colin J. Brislawn and Regina
                  Lamendella and Yoshiki Vázquez-Baeza and William
                  A. Walters and Lisa M. Bramer and Mauro D'Amato and
                  Ferdinando Bonfiglio and Daniel McDonald and Antonio
                  Gonzalez and Erin E. McClure and Mitchell
                  F. Dunklebarger and Rob Knight and Janet K. Jansson},
  title =	 {Dynamics of the human gut microbiome in inflammatory
                  bowel disease},
  journal =	 {{Nature Microbiology}},
  year =	 2017,
  volume =	 2,
  number =	 17004,
  month =	 {Feb.},
  doi =		 {10.1038/nmicrobiol.2017.4},
  url =		 {http://www.nature.com/articles/nmicrobiol20174},
}

@article{Halfvarson_2017,
  title =	 {Dynamics of the human gut microbiome in inflammatory
                  bowel disease},
  author =	 {Jonas Halfvarson and Colin J. Brislawn and Regina
                  Lamendella and Yoshiki Vázquez-Baeza and William
                  A. Walters and Lisa M. Bramer and Mauro D'Amato and
                  Ferdinando Bonfiglio and Daniel McDonald and Antonio
                  Gonzalez and Erin E. McClure and Mitchell
                  F. Dunklebarger and Rob Knight and Janet K. Jansson},
  journal =	 {{Nature Microbiology}},
  year =	 2017,
  volume =	 2,
  month =	 {Feb.},
  doi =		 {10.1038/nmicrobiol.2017.4},
  url =		 {http://www.nature.com/articles/nmicrobiol20174},
}

@Article{Jalanka-Tuovinen11,
  author =	 {Jonna Jalanka-Tuovinen and Anne Salonen and Janne
                  Nikkil{\"a} and Outi Immonen and Riina Kekkonen and
                  Leo Lahti and Airi Palva and Willem M. de Vos},
  title =	 {Intestinal microbiota in healthy adults: Temporal
                  analysis reveals individual and common core and
                  relation to intestinal symptoms},
  journal =	 {{PLoS One}},
  year =	 2011,
  volume =	 6,
  number =	 7,
  pages =	 {e23035},
  doi =		 {10.7717/peerj.32}
}

@article{Lahti11rpa,
  author =	 {Leo Lahti and Laura L. Elo and Tero Aittokallio and
                  Samuel Kaski},
  title =	 {Probabilistic Analysis of Probe Reliability in
                  Differential Gene Expression Studies with Short
                  Oligonucleotide Arrays},
  journal =	 {{IEEE/ACM Transactions on Computational Biology and
                  Bioinformatics}},
  year =	 2011,
  volume =	 8,
  number =	 1,
  pages =	 {217--225},
  month =	 {Jan.-Mar.},
  doi =		 {10.1109/TCBB.2009.38},
  url =
                  {http://www.computer.org/portal/web/csdl/doi/10.1109/TCBB.2009.38},
  publisher =	 {IEEE Computer Society},
  address =	 {Los Alamitos, CA, USA},
  annote =	 {Open source implementation:
                  http://bioconductor.org/packages/release/bioc/html/RPA.html}
}

@Article{Lahti13nar,
  author =	 {Leo Lahti and Aurora Torrente and Laura L Elo and
                  Alvis Brazma and Johan Rung},
  title =	 {A fully scalable online pre-processing algorithm for
                  short oligonucleotide microarray atlases},
  journal =	 {Nucleic Acids Research},
  volume =	 41,
  number =	 10,
  year =	 2013,
  pages =	 {e110},
  doi =		 {10.1093/nar/gkt229},
  note =	 {Implementation available through Bioconductor RPA
                  package.}
}

@Article{Lahti13provasI,
  author =	 {Leo Lahti and Anne Salonen and Riina A. Kekkonen and
                  Jarkko Salojarvi and Jonna Jalanka-Tuovinen and Airi
                  Palva and Matej Orešič and Willem M. de Vos},
  title =	 {{Associations between the human intestinal
                  microbiota, Lactobacillus rhamnosus GG and serum
                  lipids indicated by integrated analysis of
                  high-throughput profiling data}},
  journal =	 {PeerJ},
  year =	 2013,
  volume =	 1,
  pages =	 {e32},
  doi =		 {10.7717/peerj.32},
  pmid =	 23638368
}

@Article{Lahti_2013,
  title =	 {A fully scalable online-preprocessing algorithm for
                  short oligonucleotide microarray atlases},
  author =	 {Leo Lahti and Aurora Torrente and Laura L. Elo and
                  Alvis Brazma and Johan Rung},
  journal =	 {Nucleic Acids Research},
  year =	 2013,
  volume =	 41,
  issue =	 10,
  pages =	 {e110},
  note =	 {R/BioC:
                  http://bioconductor.org/packages/release/bioc/html/RPA.html},
  url =		 {http://nar.oxfordjournals.org/content/41/10/e110},
}

@Article{Langfelder_2008,
  author =	 {Peter Langfelder and Steve Horvath},
  title =	 {WGCNA: an R package for weighted correlation network
                  analysis},
  journal =	 {BMC Bioinformatics},
  year =	 2008,
  number =	 1,
  pages =	 559,
  pubmedid =	 19114008,
}

@Article{Langfelder_2012,
  title =	 {Fast {R} Functions for Robust Correlations and
                  Hierarchical Clustering},
  author =	 {Peter Langfelder and Steve Horvath},
  journal =	 {Journal of Statistical Software},
  year =	 2012,
  volume =	 46,
  number =	 11,
  pages =	 {1--17},
  url =		 {http://www.jstatsoft.org/v46/i11/},
}

@Article{Meyer_2008,
  title =	 {MINET: An open source R/Bioconductor Package for
                  Mutual Information based Network Inference},
  author =	 {Patrick E. Meyer and Frederic Lafitte and Gianluca
                  Bontempi},
  journal =	 {BMC Bioinformatics},
  year =	 2008,
  volume =	 9,
  url =		 {http://www.biomedcentral.com/1471-2105/9/461},
}

@Article{OKeefe15,
  author =	 {SJD O'Keefe and JV Li and L Lahti and J Ou and F
                  Carbonero and K Mohammed and JM Posma and J Kinross
                  and E Wahl and E Ruder and K Vipperla and V Naidoo
                  and L Mtshali and S Tims and PGB Puylaert, J DeLany
                  and A Krasinskas and AC Benefiel and HO Kaseb and K
                  Newton and JK Nicholson and WM de Vos and HR Gaskins
                  and EG Zoetendal},
  title =	 {Fat, Fiber and Cancer Risk in African, Americans and
                  Rural Africans},
  journal =	 {Nature Communications},
  year =	 2015,
  volume =	 6,
  pages =	 6342,
  month =	 {Apr},
  doi =		 {10.1038/ncomms7342},
  note =	 {Top science article in Guardian on the release day.}
}

@Book{MASS,
    title = {Modern Applied Statistics with S},
    author = {W. N. Venables and B. D. Ripley},
    publisher = {Springer},
    edition = {Fourth},
    address = {New York},
    year = {2002},
    note = {ISBN 0-387-95457-0},
    url = {http://www.stats.ox.ac.uk/pub/MASS4},
}

@Manual{dplyr,
  title =	 {{dplyr: A Grammar of Data Manipulation}},
  author =	 {Hadley Wickham and Romain Francois},
  year =	 2016,
  note =	 {R package version 0.5.0},
  url =		 {https://CRAN.R-project.org/package=dplyr}
}



@Manual{RColorBrewer,
  title =	 {RColorBrewer: ColorBrewer Palettes},
  author =	 {Erich Neuwirth},
  year =	 2014,
  note =	 {R package version 1.1-2},
  url =		 {https://CRAN.R-project.org/package=RColorBrewer},
}



@Manual{tidyr,
  author =	 {Hadley Wickham},
  title =	 {{tidyr: Easily Tidy Data with spread and gather
                  Functions}},
  year =	 2017,
  note =	 {R package version 0.6.3},
  url =		 {https://CRAN.R-project.org/package=tidyr}
}



@Manual{Oksanen_2015,
  title =	 {vegan: Community Ecology Package},
  author =	 {Jari Oksanen and F. Guillaume Blanchet and Roeland
                  Kindt and Pierre Legendre and Peter R. Minchin and
                  R. B. O'Hara and Gavin L. Simpson and Peter Solymos
                  and M. Henry H. Stevens and Helene Wagner},
  year =	 2015,
  note =	 {R package version 2.2-1},
  url =		 {http://CRAN.R-project.org/package=vegan},
}

@Article{Salonen12cmi,
  author =	 {Anne Salonen and Jarkko Saloj{\"a}rvi and Leo Lahti
                  and and Willem M. de Vos},
  title =	 {The adult intestinal core microbiota is determined
                  by analysis depth and health status},
  journal =	 {Clinical Microbiology and Infection},
  year =	 2012,
  volume =	 18,
  number =	 {Suppl. 4},
  pages =	 {16–20},
  doi =		 {10.1111/j.1469-0691.2012.03855.x}
}

@Article{Shetty2017,
  author =	 {Shetty, SA and Hugenholtz, F and Lahti, L and Smidt,
                  H and de Vos, WM and Danchin, A},
  title =	 {Intestinal microbiome landscaping: Insight in
                  community assemblage and implications for microbial
                  modulation strategies},
  journal =	 {FEMS Microbiology Reviews},
  year =	 2017,
  pages =	 {{fuw045}},
  doi =		 {10.1093/femsre/fuw045}
}

@Manual{Temple_Lang_2014,
  title =	 {RCurl: General network (HTTP/FTP/...) client
                  interface for R},
  author =	 {Duncan {Temple Lang}},
  year =	 2014,
  note =	 {R package version 1.95-4.3},
  url =		 {http://CRAN.R-project.org/package=RCurl},
}

@Article{Wickham_2007,
  author =	 {{Wickham} and {Hadley}},
  journal =	 {Journal of Statistical Software},
  number =	 12,
  title =	 {Reshaping data with the reshape package},
  url =		 {http://www.jstatsoft.org/v21/i12/paper},
  volume =	 21,
  year =	 2007,
}

@Book{Wickham_2009,
  author =	 {Hadley Wickham},
  title =	 {ggplot2: elegant graphics for data analysis},
  publisher =	 {Springer New York},
  year =	 2009,
  isbn =	 {978-0-387-98140-6},
  url =		 {http://had.co.nz/ggplot2/book},
}

@Article{Wickham_2011,
  title =	 {The Split-Apply-Combine Strategy for Data Analysis},
  author =	 {Hadley Wickham},
  journal =	 {Journal of Statistical Software},
  year =	 2011,
  volume =	 40,
  number =	 1,
  pages =	 {1--29},
  url =		 {http://www.jstatsoft.org/v40/i01/},
}

@Article{lahti14natcomm,
  author =	 {Leo Lahti and Jarkko Salojarvi and Anne Salonen and
                  Marten Scheffer and Willem M. de Vos},
  title =	 {Tipping elements in the human intestinal ecosystem},
  journal =	 {Nature Communications},
  year =	 2014,
  volume =	 5,
  pages =	 4344,
  month =	 {July},
  doi =		 {10.1038/ncomms5344}
}

@Book{rcore13,
  author =	 {{R Core Team}},
  title =	 {R: A language and environment for statistical
                  computing},
  publisher =	 {R Foundation for Statistical Computing},
  year =	 2013,
  isbn =	 {ISBN 3-900051-07-0},
  address =	 {Vienna, Austria},
  url =		 {http://www.R-project.org/},
}

@Article{salonen14,
  author =	 {Anne Salonen and Leo Lahti and Jarkko Saloj{\"a}rvi
                  and Grietje Holtrop and Katri Korpela and Sylvia
                  Duncan and Priya Date and Alexandra Johnstone and
                  Gerald Lobley and Petra Louis and Harry Flint and
                  Willem M. de Vos},
  title =	 {Impact of diet and individual variation on
                  intestinal microbiota composition and fermentation
                  products in obese men},
  journal =	 {ISME Journal},
  year =	 2014,
  volume =	 8,
  pages =	 {2218--2230},
  url =
                  {http://www.nature.com/ismej/journal/vaop/ncurrent/full/ismej201463a.html},
  doi =		 {10.1038/ismej.2014.63}
}

@Book{venables02,
  author =	 {W. N. Venables and B. D. Ripley},
  title =	 {Modern Applied Statistics with S},
  publisher =	 {Springer},
  year =	 2002,
  isbn =	 {ISBN },
  address =	 {New York},
  edition =	 {fourth},
  isbn =	 {ISBN },
}
